Adams Lab: Publications

Publications

Publications are indexed in chronological order beginning with the most recent publications last. Publication supplements and data sets are listed under the Data section.

Present-251

250-201

200-151

150-101

100-51

50-1

Index

Publication

292

Blumer-Schuette, S., Kataeva, I., Westpheling, J., Adams, M. W. W. and Kelly, R. M. (2008) "Extremely thermophilic microorganisms for biomass conversion: status and prospects" Curr. Op. Biotechnology 19, 1-8

291

Jenney, F. E., Jr., and Adams, M. W. W. (2008) "Hydrogenases of the model hyperthermophiles" Ann. N.Y. Acad. Sci. 1125, 252-266

290

Bansal, S., Miao, X., Adams, M. W. W., Prestegard, J. H. and Valafar, H. (2008) "Rapid classification of protein structure models using unassigned backbone RDCs and probability density profile analysis (PDPA)" J. Mag. Resonance (in press)

289

Shaw, A. J., Jenney, F. E., Jr., Adams, M. W. W. and Lynd, L. (2008) "Enzymatic and genomic evidence for end-product pathways in Thermoanaerobacterium saccharolyticum" Enz. Micro. Technol. (in press)

288

Trauger, S. A., Kalisak, E., Kalisiak, J., Morita, H., Weinberg, M.V., Menon, A. L., Poole, F. L., Adams, M. W. W. and Siuzdak, G. (2008) Correlating the Transcriptome, Proteome, and Metabolome in the Environmental Adaptation of a Hyperthermophile. J. Proteome. Res. Feb 2; [Epub ahead of print]

287

Jenney, F. E., Jr. and Adams, M. W. W. (2008) "The impact of structural genomics on extremophiles (and vice versa)" Extremophiles 12, 39-50

286

Dey, A., Jenney, F. E., Jr., Adams, M. W. W., Babini, E., Takahashi, Y., Fukuyama, K., Hodgson, K. O., Hedman, B. and Solomon, E. I. (2007) "Solvent tuning of electrochemical potentials in the active sites of HiPIP versus ferredoxin" Science 318, 1464-1468

285

Chou, C. J., Shockley, K. R., Conners, S. B., Lewis, D. L., Comfort, D. A., Adams, M. W. W. and Kelly, R.M. (2007) "Impact of substrate glycoside linkage and elemental sulfur on bioenergetics and hydrogen production by the hyperthermophilic archaeon Pyrococcus furiosus" Appl. Environ. Microbiol. 73, 6842-6853

284

Dey, A., Jenney Jr., F. E., Adams, M. W. W., Johnson, M. K., Hodgson, K. O., Hedman, B. and Solomon, E. I. "Sulfur K-edge XAS and DFT calculations on superoxide reductase: Role of the axial thiolate in reactivity" J. Am. Chem. Soc. 129, 12418-31

283

Vondrasek, J., Kubar, T., Jenney, F. E. Jr., Adams, M. W. W., Kozisek, M., Cerny, J., Sklenar, V. and Hobza, P. (2007) "Dispersion interactions govern the strong thermal stability of a protein" Chemistry 13, 9022-9027

282

Kelley, L. L., Dillard, B. D., Tempel, W., Chen, L., Shaw, N., Lee, D., Newton, M. G., Sugar, F. J., Jenney, F. E. Jr., Lee, H. S., Shah, C., Poole, F. L., Adams, M. W. W., Richardson, J. S., Richardson, D. C., Liu, Z. J., Wang, B. C. and Rose, J. (2007) "Structure of the hypothetical protein PF0899 from Pyrococcus furiosus at 1.85 A resolution" Acta Cryst. 63, 549-552

281

Cacciapuoti, G., Porcelli. M., Moretti, M. A., Zappia,V., Liu, Z.-J., Tempel, W., Schubot, F., Rose, J. P., Wang, B.-C., Brereton, P. S., Jenney, F. E. and Adams, M. W. W. (2007) "The first agmantine/cadaverine aminopropyl transferase: biochemical and structural characterization of the enzyme involved in polyamine biosynthesis in the hyperthermophilic archaeon Pyrococcus furiosus" J. Bacteriol. 189, 6057-6067

280

Zhu, J., Fu, X., Koo, Y. D., Zhu, J. K., Jenney, F. E., Jr., Adams, M. W. W., Zhu, Y., Shi, H., Yun, D. J., Hasegawa, P. M. and Bressan, R. A. (2007) "An enhancer mutant of Arabidopsis salt overly sensitive 3 mediates both ion homeostasis and the oxidative stress response" Mol. Cell. Biol. 27, 5214-5224

279

Gerwe, B., Kelley, L.-L. K., Dillard, B. D., Lai, T., Liu, Z.-J., Tempel, W., Chen, L., Habel, J., Lee, D., Jenney, F. E. Jr., Sugar, F. J., Richardson, J. S., Richardson, D. C., Newton, M. G., Wang, B.-C., Adams, M. W. W. and Rose, J. P. (2007) "Structural and transcriptional analyses of a purine nucleotide-binding protein from Pyrococcus furiosus: a component of a novel, membrane-bound multiprotein complex unique to this hyperthermophilic archaeon" J. Struct. Funct. Genomics 8, 1-10

278

Zhang, Y. H. P., Evans, B. R., Mielenz, J. R., Hopkins, R. C. and Adams, M. W. W. (2007) "High yield hydrogen production from starch and water by a synthetic enzyme pathway" PLoS One 5, e456 (1-6)

277

Schut, G., Bridger, S. L. and Adams, M. W. W. (2007) "Insights into the metabolism of elemental sulfur by the hyperthermophilic archaeon Pyrococcus furiosus: characterization of a coenzyme A-dependent NAD(P)H sulfur oxidoreductase" J. Bacteriol. 189, 4431-4441

276

Adams, M. W. W., Jenney, F. E. Jr., Chou, C.-J., Hamilton-Brehm, S., Poole, F. L., Shockley, K. R., Tachdjian, S. and Kelly, R. M. (2007) Transcriptomics, Proteomics and Structural Genomics of Pyrococcus furiosus. Archaea: Evolution, Physiology, and Molecular Biology (Garrett, R. and Klenk, H.-P., eds.), Blackwell, 239-246

275

Jenney, F. E. Jr., Tachdjian, S., Chou, C.-J., Kelly, R. M. and Adams, M. W. W. (2007) Functional Genomics. Archaea: Molecular and Cellular Biology (Cavicchioli, R., ed.) Blackwell, 434-462

274

Tran, T. T., Dam, P., Su, P., Poole, F. P., Adams, M. W. W., Zhou, G. T. and Xu, Y. (2007) "Operon prediction in Pyrococcus furiosus" Nucleic Acid Res. 35, 11-20

273

Wang, X., Lee, H.-S., Sugar, F., Jenney, F. E., Adams, M. W. W. and Prestegard, J. H. (2007) PF0610, a novel winged HTH variant possessing a rubredoxin-like Zn-ribbon motif from the hyperthermophilic archaeon, Pyrococcus furiosus" Biochemistry 46, 752-761

272

Tan, M. L., Bizzarri, A. R., Xiao, Y., Cannistraro, S., Ichiye, T., Manzoni, C., Cerullo,G., Adams, M. W. W., Jenney, F. E. and Cramer, S. P. (2007) "Observation of terahertz vibrations in Pyrococcus furiosus rubredoxin via impulsive coherent vibrational spectroscopy and nuclear resonance vibrational spectroscopy - Interpretation by molecular mechanics" J. Inorg. Biochem. 101, 375-384

271

Mayer, K. L., Qu, Y., Bansal, S., Leblond, P. D., Jenny, F. E. Jr., Brereton, P. S., Adams, M. W. W., Xu, Y, and Prestegard, J. H. (2006) "Structure of a novel protein from backbone-centered NMR data and NMR-assisted structure prediction" Proteins 65, 480-489

270

Yang, T.-C. , McNaughton, R. L., Clay, M. D., Jenney, Jr., F. E., Krishnan, R., Kurtz, Jr., D. M., Adams, M. W. W., Johnson, M. K. and Hoffman, B. M. (2006) "Comparing the electronic properties of the low-spin cyano-ferric [Fe(N4)(Cys)] active sites of superoxide reductase and P450cam using ENDOR spectroscopy and DFT calculations" J. Am. Chem. Soc. 128, 16566-16578

269

Tucker, G. S., Brown, H. M., Fryer, P. J., Cos, P. W., Poole, F. L., Lee, H.-S. and Adams, M. W. W. (2006) "A sterilisation time-temperature integrator based on amylase from the hyperthermophilic organism Pyrococcus furiosus" Innov. Food Sci. Emerg. Tech. 8, 63-72

268

Lee, H.-S., Shockley, K. R., Schut, G. J., Conners, S. B., Montero, C. I., Johnson, M. R., Chou, C.-J., Bridger, S. L., Wigner, N., Brehm, S. D., Jenney, F. E., Jr., Comfort, D. A., Kelly, R. M. and Adams, M. W. W. (2006) "Transcriptional and biochemical analysis of starch metabolism in the hyperthermophilic archaeon Pyrococcus furiosus" J. Bacteriol. 188, 2115-2125

267

Clay, M. D., Yang, T. C., Jenney, F. E. Jr., Kung, I. Y., Cosper, C. A., Krishnan, R., Kurtz, D. M., Jr., Adams, M. W. W., Hoffman, B. M., and Johnson, M. K. (2006) "Geometries and electronic structures of cyanide adducts of the non-heme iron active site of superoxide reductases: vibrational and ENDOR studies" Biochemistry 17, 427-438

266

Poole, F. L., Gerwe, B. A., Hopkins, R. C., Schut, G. J., Weinberg, M. V., Jenney, F. E., Jr., and Adams, M. W. W. (2005) "Defining genes in the genome of the hyperthermophilic archaeon Pyrococcus furiosus: implications for all microbial genomes" J. Bacteriol. 187, 7325-7332

265

Xiao, Y., Dey, A., Wang, H. George, S. J., Smith, M. C., Adams, M. W. W., Jenney, F. E., Jr., Sturhahn, W., Alp, E. E., Yoda, J., Solomon, E. I., and Cramer, S. P. (2005) Normal mode analysis of Pyrococcus furiosus rubredoxin via nuclear resonant vibrational spectroscopy (NRVS) and resonance Raman spectroscopy" J. Am. Chem. Soc. 127, 14596-145606

264

Hamilton-Brehm, S., Schut, G. and Adams, M. W. W. (2005) "Metabolic and evolutionary relationships amongst Pyrococcus species: genetic exchange in the same hydrothermal vent environment" J. Bacteriol. 187, 7492-7499

263

Eichler, J. and Adams, M. W. W. (2005) "Post-translational protein modification in archaea" Mole. Microbiol. 69, 393-425

262

Wang, B. C., Adams, M. W. W., Dailey, H., DeLucas, L., Luo, M., Rose, J., Bunzel, R., Dailey, T., Habel, J., Horanyi, P., Jenney, F. E., Kataeva, I., Li, S., Lin, D., Liu, Z.-J., Luan, C. H., Mayer, M., Nagy, L., Newton, M. G., Ng, J., Poole, F., Shah, A. and Xu, H. (2005) "Protein production and crystallization at the SECSG – an overview" J. Struct. Funct. Genomics 6, 233-243

261

Scott, R. A., Shokes, J. E., Cosper, N. J., Jenney, F. E. and Adams, M. W. W. (2005) Bottlenecks and roadblocks in high-throughput XAS for structural genomics. J. Synchrotron Res. 5, 241-254

260

Valafar, H., Mayer, K. L., Bougault, C. M., LeBlond, P. D., Jenney, F. E., Jr., Brereton, P. S., Adams, M. W. W. and Prestegard, J. H. (2005) Backbone solution structures of proteins using residual dipolar couplings: Application to a novel structural genomics target" J. Struct. Funct. Genomics 5, 241-254

259

Sugar, F. J., Jenney, F. E., Jr., Poole, F. L. Brereton, P. S., Izumi, M., Shah, C. and Adams., M. W. W. (2005) "Comparison of small- and large-scale expression of selected Pyrococcus furiosus genes as an aid to high-throughput protein production" J. Struct. Funct. Genomics 5, 241-254

258

Story, S. V. Shah, C., Jenney, F. E. and Adams, M. W. W. (2005) " Characterization of a novel zinc-containing lysine aminopeptidase from the hyperthermophilic archaeon Pyrococcus furiosus" J. Bacteriol. 187, 2077-2083

257

Jenney, Jr. F. E., Brereton, P. S., Izumi, M., Poole II, F. L., Shah, C., Sugar, F. J., Lee, H.-S. and Adams , M. W. W. (2005) "High throughput production of Pyrococcus furiosus proteins - considerations for metalloproteins" J. Synchrotron Radiation 12, 19-22

256

Johnston , W., Cooney, M. J., Liaw, B. Y., Sapra, R. and Adams, M. W. W. (2005) "The design and characterization of redox enzyme electrodes: new perspectives on established techniques with application to an extremophilic hydrogenase" Enz. Microb. Tech. 36, 540-549

255

Kurihara, K., Tanaka, I. , Chatake, T., Adams, M. W. W., Jenney Jr., F. E., Moiseeva, N., Bau, R. and Niimura, N. (2004) "Neutron crystallographic study on rubredoxin from Pyrococcus furiosus by BIX-3, a single-crystal diffractometer for biomacromolecules" Proc. Nat. Acad. Sci. 101, 11215-11220

254

Grunden, A. M., Jenney, F. E., Jr., Ma, K., Ji, M., Weinberg, M. V. and Adams, M. W. W. (2005) "In vitro reconstitution of a NADPH-dependent superoxide reduction pathway from Pyrococcus furiosus" Appl. Environ. Microbiol. 71, 1522-1530

253

Weinberg, M. V., Jenney, F. E., Jr., Cui, X. and Adams , M. W. W. (2004) "Rubrerythrin from the hyperthermophilic archaeon Pyrococcus furiosus is a rubredoxin-dependent, iron-containing peroxidase" J. Bacteriol. 186, 7888-7895

252

Weinberg, M. V., Schut, G. J., Brehm, S., Datta, S. and Adams, M. W. W. (2005) Cold shock of a hyperthermophilic archaeon: Pyrococcus furiosus exhibits multiple responses to a suboptimal growth temperature with a key role for membrane-bound glycoproteins. J Bacteriol. 187, 336-348 (Supplementary Material)